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L1-seq and genome-wide SNP genotyping in a multiethnic Asian population

ABSTRACT:

Insertions of the human-specific subfamily of LINE-1 (L1) retrotransposon are highly polymorphic across individuals and can critically influence the human transcriptome. We hypothesized that L1 insertions could represent genetic variants determining important human phenotypic traits, and performed an integrated analysis of L1 elements and single nucleotide polymorphisms (SNPs) in several human populations. We found that a large fraction of L1s were in high linkage disequilibrium (LD) with their surrounding genomic regions and that they were well-tagged by SNPs. However, L1 variants were only partially captured by SNPs on standard SNP arrays, so that their potential phenotypic impact would be frequently missed by SNP array-based genome-wide association studies. We next identified potential phenotypic effects of L1s by looking for signatures of natural selection linked to L1 insertions; significant extended haplotype homozygosity (EHH) was detected around several L1 insertions. This suggests that some of these L1 insertions may have been the target of recent positive selection.

PROVIDER: phs000732 | dbGaP |

SECONDARY ACCESSION(S): PRJNA242733PRJNA242788

REPOSITORIES: dbGaP

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Dataset's files

Source:

			Action	DRS
	GapExchange_phs000732.v1.p1.xml	Xml
	dbGaPEx2.1.5.xsd	Other
	Study_Report.phs000732.LINE_1Retrotransposons.v1.p1.MULTI.pdf	Pdf
	manifest_phs000732.LINE_1Retrotransposons.v1.p1.c1.GRU.pdf	Pdf
	datadict_v2.xsl	Other

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Dataset Information

L1-seq and genome-wide SNP genotyping in a multiethnic Asian population

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